Identification of Molecular Markers That Are Specific to the Class Thermoleophilia.

Danyu Hu,Beile Gao,Yang Zang,Yingjin Mao

doi:10.3389/fmicb.2019.01185

Abstract

The class Thermoleophilia is one of the deep-rooting lineages within the Actinobacteria phylum and metagenomic investigation of microbial diversity suggested that species associated with the class Thermoleophilia are abundant in hot spring and soil samples. However, very few species of this class have been cultivated and characterized. Our understanding of the phylogeny and taxonomy of Thermoleophilia is solely based on 16S rRNA sequence analysis of limited cultivable representatives, but no other phenotypic or genotypic characteristics are known that can clearly discriminate members of this class from the other taxonomic units within the kingdom bacteria. This study reports phylogenomic analysis for 12 sequenced members of this class and clearly resolves the interrelationship of not yet cultivated species with reconstructed genomes and known type species. Comparative genome analysis discovered 12 CSIs in different proteins and 32 CSPs that are specific to all species of this class. In addition, a large number of CSIs or CSPs were identified to be unique to certain lineages within this class. This study represents the first and most comprehensive phylogenetic analysis of the class Thermoleophilia, and the identified CSIs and CSPs provide valuable molecular markers for the identification and delineation of species belonging to this class or its subordinate taxa.

Highlights

The class Thermoleophilia is one of the deep-rooting lineages within the Actinobacteria phylum and it has only recently been recognized as independent from the class Rubrobacteria (Zhi et al, 2009; Gao and Gupta, 2012b; Ludwig et al, 2012; Suzuki and Whitman, 2012)
The order Thermoleophilales only contains one family Thermoleophilaceae with a single genus Thermoleophilum. Species of this genus are small regular rods, moderately thermophilic, and obligately aerobic (Suzuki and Whitman, 2012). Their distinct feature is growth restriction to substrate n-alkanes (Zarilla and Perry, 1986), these species are named as heat- and oil-loving microbes, “Thermoleophilum.” While Thermoleophilum species are generally isolated from hot springs, members of the second order Solirubrobacterales are mainly detected in soil samples, and they exhibit more species diversity and different phenotypic characteristics
Metagenomic studies suggest that species of the class Thermoleophilia are abundant in hot spring and soil samples and they play an important role in biogeochemical cycling, very few studies have been performed on the phylogeny of this deep branch of Actinobacteria

Summary

Introduction

The class Thermoleophilia is one of the deep-rooting lineages within the Actinobacteria phylum and it has only recently been recognized as independent from the class Rubrobacteria (Zhi et al, 2009; Gao and Gupta, 2012b; Ludwig et al, 2012; Suzuki and Whitman, 2012). The order Thermoleophilales only contains one family Thermoleophilaceae with a single genus Thermoleophilum Species of this genus are small regular rods, moderately thermophilic, and obligately aerobic (Suzuki and Whitman, 2012). Their distinct feature is growth restriction to substrate n-alkanes (Zarilla and Perry, 1986), these species are named as heat- and oil-loving microbes, “Thermoleophilum.” While Thermoleophilum species are generally isolated from hot springs, members of the second order Solirubrobacterales are mainly detected in soil samples, and they exhibit more species diversity and different phenotypic characteristics. Their preferred carbon sources are more diverse, including complex proteinaceous substrates, many sugars and a few other compounds (Foesel et al, 2016)

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